Metadata-Version: 2.4
Name: pudupy
Version: 1.0.0b5
Summary: Protocol Unified Design Unit
Author-email: Gonzalo Vidal <govi9038@colorado.edu>, Oscar Rodriguez <osro6012@colorado.edu>
Maintainer-email: Gonzalo Vidal <govi9038@colorado.edu>, Oscar Rodriguez <osro6012@colorado.edu>
License: MIT License
        
        Copyright (c) 2022 Rudge Lab
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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        SOFTWARE.
        
Project-URL: Homepage, https://github.com/MyersResearchGroup/PUDU
Project-URL: Bug Tracker, https://github.com/MyersResearchGroup/PUDU/issues
Keywords: pudu,lab,automation,opentrons,synthetic biology
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: opentrons>=8.4.1
Requires-Dist: xlsxwriter>=3.2.5
Requires-Dist: sbol2>=1.4.1
Provides-Extra: test
Requires-Dist: pytest>=7.0.0; extra == "test"
Requires-Dist: pytest-cov; extra == "test"
Dynamic: license-file

# PUDU
Welcome to the PUDU (Protocol Unified Design Unit) repository, our Python package for liquid handling robot control on Synthetic Biology workflows.


<img src="https://github.com/MyersResearchGroup/PUDU/blob/main/images/PUDU_Logo.png#gh-light-mode-only" alt="PUDU logo" width="250"/>
<img src="https://github.com/MyersResearchGroup/PUDU/blob/main/images/PUDU_Logo_dark.png#gh-dark-mode-only" alt="PUDU night logo" width="250"/>

## *The art of automated liquid handling*

As you may have noticed, our logo features a beautiful pudu _[(Pudu puda)](https://en.wikipedia.org/wiki/Pudu)_; a deer native to the southern forests of Chile and Argentina known for being the smallest deer of the world[.](https://youtu.be/xRQnJyP77tY)
This package intends to make the code to program liquid handling robots as small and simple as possible.

## No Installation required protocols

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.

### Calibrate your plate reader using PUDU script libre

[Human protocol](https://github.com/RudgeLab/PUDU/blob/main/protocols/Multicolor_fluorescence_per_particle_calibration_protocol_igem/Automated_protocol_user_instructions.xlsx) (Excel to set the OT2 deck)

[Robot protocol](https://github.com/RudgeLab/PUDU/blob/main/scripts/run_iGEM2022_rgb_od_libre.py) (Python script to run the OT2)

Reference: [Original protocol](https://old.igem.org/wiki/images/a/a4/InterLab_2022_-_Calibration_Protocol_v2.pdf) (2022 iGEM InterLab study)

## Recommended workflow

- 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.py ` for example [[instructions](https://support.opentrons.com/s/article/Simulating-OT-2-protocols-on-your-computer?)]
- 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! :wink: )

## Installation

### Computer installation

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.

### OT-2 installation

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](https://support.opentrons.com/s/article/Setting-up-SSH-access-to-your-OT-2)]

Afterwards you can just SSH into the OT2 [[instructions](https://support.opentrons.com/s/article/Connecting-to-your-OT-2-with-SSH)]

then in the OT-2 terminal run:

`pip install pudupy`

## Documentation

 Please visit our documentation with API reference at Read the Docs (TODO)

## Tutorials

TODO
