Team:UC Davis/Collaborations

Opentrons Team Collaboration

As part of an Opentrons sponsorship of the iGEM competition, our team was awarded an Opentrons OT-2 pipetting robot. For our main collaboration initiative, we reached out to all 20 iGEM teams that were selected, in both 2018 and 2019, as the winners of the Opentrons OT-2 Pipetting Robot.

Our goal for this Inter-Lab collaboration was to collect data and determine the accuracy of the OT-2 compared to humans. To do this, we designed a protocol to perform sets of Serial Dilutions of Fluorescein and Microsphere solutions by hand and with the OT-2. Six iGEM teams collaborated for this study of the OT-2.

This interlab collaboration will benefit both the teams involved and future Opentrons customers by providing information on the precision of the OT-2. A secondary goal for this collaboration was to facilitate communication between iGEM teams who have received the Opentrons OT-2. We are currently developing more protocols that will be beneficial in the iGEM context.

Inter-Lab Communication

We collected contact information of all the teams that had been awarded Opentrons OT-2 Pipetting Robots. We then contacted the teams inviting them to join our collaboration. With help from Marburgh, we created a Slack Channel for easy communication between the teams. This allowed the iGEM teams to share protocols and troubleshoot problems with their OT-2's.

Thank you to the teams who collaborated for this study:

Marburg University
Stony Brook University
University of Victoria Wellington
TU Delft
University of Leiden
University of Düsseldorf
OUC China


Developed OT-2 Protocol

Using the Protocol designer beta application by Opentrons, we designed a custom protocol for use during our study. This protocol automated the Serial Dilution Standardization tests provided by iGEM, and used only labware provided by Opentrons and solutions provided by iGEM.

We shared this protocol with all the OT2 winners and asked that they performed the protocol using the OT2 three times using Fluorescein and once using Microspheres, then repeat the experiment by hand. Then, using plate readers, teams measured the Abs600 and Fluorescence of their plates.

After completing their dilutions, teams sent us their data. We analyzed the collected data to draw conclusions about the accuracy of OT-2 pipetting robots. We standardized the data by calculating the MFEL and particles per Abs600. Using the standardized data we plotted points using ggplot2 in R studio and calculated the R^2 values of the serial dilution standardization curves.

Adapted Existing iGEM Protocols

We designed a protocol to use the OT-2 to automate the iGEM calibration and measurement protocols using Fluorescein and Microspheres. We chose to automate existing serial dilution protocols rather than to write a new protocol to ensure that all teams had access to the same reagents. We used only materials that came with the Opentrons OT2 or the iGEM kit to limit variation due to lab materials.

To standardize plate reader measurements, we calculated MEFL values and absorbance per particles. This allowed the data collected using different plate readers to be standardized and plotted together.


Microsphere Data

Fluorescein Data


The Opentrons OT2 pipetting robot is a helpful lab tool for arduous and repetitive tasks. Due to the time it takes to calibrate the robot when changing between protocols, automation of lab protocols is best when a procedure is done repetitively. From the data, one may conclude that when pipetting fluids that are viscous or contain suspended particles, the OT2 is on average less accurate than a human. However, it appears that there was one trial in which the OT2 trial was significantly out of the expected range. This abnormality may be explained by calibration error of the OT2. The OT2 additionally faces challenges associated with pipetting solutions with suspended particles. Suspended particles may not stay in suspension; while a user may be able to observe if their solution is homogeneous, a robot is unable to see the solution and make an accurate determination. In tasks that don’t require specialized pipetting practices, the OT2 just as effective as a lab member. When using the Opentrons OT2 pipetting robot, it is best to plan experiments in a way which automation can be beneficial and to build in controls against some level of pipetting error.

We found that some simple modifications to the user interface of the OT2 would improve the usability of the OT2. These include a liquid tracking feature to prevent contamination of the pipette when aspirating from deep wells, and a feature to mix or agitate source wells to prevent particles from settling.