Welcome to the PUDU (Protocol Unified Design Unit) repository, our Python package for liquid handling robot control on Synthetic Biology workflows.
As you may have noticed, our logo features a beautiful pudu (Pudu puda); a deer native to the southern forests of Chile and Argentina known for being the smallest deer of the world. This package intends to make the code to program liquid handling robots as small and simple as possible.
Some scripts have "libre" in their name, this means that users can modify these scripts and use them to run protocols whithout the need to install PUDU.
Human protocol (Excel to set the OT2 deck)
Robot protocol (Python script to run the OT2)
Reference: Original protocol (2022 iGEM InterLab study)
- Install PUDU in your computer
- Install PUDU in the OT2 that will perform the automation
- Develop protocols in your computer
- To simulate your protocols you can open the PUDU folder in your terminal and run
opentrons_simulate ./scripts/run_Loop_assembly.pyfor example [instructions] - Transfer the script file (.py) to the computer used to run the protocol on the OT2 (if its the same, omit)
- Load the script file (.py) on the Opentrons App
- Follow Oppentrons App instruction
- Set the OT2 deck with the information provided by the Opentrons App and PUDU human readable dictionaries at the top of the simulation output.
- Run your protocol and enjoy automation (Now you have more time to design your next experiment! 😉 )
Installing PUDU is way easier than pronuncing it!
Run:
pip install pudupy
This code can be executed in the terminal and in jupyter notebooks.
For more details please refer to our Wiki (TODO) for installation instructions and developer guides.
To install it on an OT2 you first need to SSH into it.
Only the first time you need to set the SSH connection [instructions]
Afterwards you can just SSH into the OT2 [instructions]
then in the OT-2 terminal run:
pip install pudupy
Please visit our documentation with API reference at Read the Docs (TODO)
TODO