Opentrons LARP protocol generator and graphical prognostic

This repository contains code to design and evaluate LARP (Ligand-assisted reprecipitation) synthesis protocols to be performed using the OT-2 liquid handler robot. The code can be evaluated using the opentrons_simulate API to verify any inconsistencies. Additionally, a graphical interface is provided to visualize the different stages of the LARP synthesis.

Example of graphical prognostic of the LARP protocol.

Installation

Clone the repository and install the required packages using the following command:

pip install -r requirements.txt

Usage

There are two ways to use the code:

1. Using the LARP Protocol Script:

   • Navigate to the protocol_scripts folder and copy the desired script to a new folder.
   • Edit the entries such as pipette tips, labware, and reagents according to your lab setup in the appropriate variables.
   • Ensure any custom labware files used by the protocol are in the same folder.
   • Run the script using Python:

     python3 larp_script_v001.py

   • If SIMULATE_MODE is set to True, the script will run in simulation mode, generating a graphical interface to visualize the different stages of the LARP synthesis. If SIMULATE_MODE is set to False, the script can be uploaded directly to the OT-2 robot.
   • Verify the run using the following command from the Opentrons API:

     opentrons_simulate larp_script_v001.py

   • Ensure the SIMULATE_MODE variable in the script is set to False and the labware JSON files are in the same folder.

   If all goes well, you can upload the script to the OT-2 robot and run the LARP synthesis.

2. Generating Protocol from Excel File:

   • In the protocol_setup folder, there is an Excel file named protocol_setup.xlsx which provides a user-friendly way to declare all necessary variables for the protocol generator.
   • Modify only the indicated cells in the Excel file to avoid errors during the generation of the final protocol script.
   • Use the xlsx_to_protocol.py script to create the final protocol script.
   • The final script can be used to generate the graphical prognostic of the LARP synthesis or be uploaded to the OT-2 robot, just as in the first method.

Conclusion

This repository provides a comprehensive solution for designing and evaluating LARP synthesis protocols using the OT-2 liquid handler robot. Whether you prefer scripting directly or using an Excel-based setup, the tools provided will help ensure accurate and efficient protocol execution.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Acknowledgments

• Brazilian funding agency CNPq for the financial support throughout this project.
• Opentrons for devoloping the OT-2 liquid handler robot and API.