Python for Hamilton liquid handling robots

Hamilton software only works on Windows, so the same goes for PyHamilton.

Developed for Hamilton STAR and STARlet on Windows XP, Windows 7, and Windows 10. VANTAGE series supported with plugin. Other robot models and operating systems not supported yet.

Contact: [email protected] for questions, ideas, or help with installation.

if __name__ == "__main__":

    from pyhamilton import HamiltonInterface, INITIALIZE
    with HamiltonInterface() as ham_int:
    
        ham_int.wait_on_response(ham_int.send_command(INITIALIZE))

Available online.

1. Install and test the standard Hamilton software suite for your system.

2. Install 32-bit python <=3.9, preferably using the executable installer at https://www.python.org/downloads/release/python-390/. Python 3.10 is known to cause an installation issue with some required pythonnet/pywin32 modules.

3. Make sure git is installed. https://git-scm.com/download/win

4. Make sure you have .NET framework 4.0 or higher installed. https://www.microsoft.com/en-us/download/details.aspx?id=17851

5. Update your pip and setuptools.

   > python -m pip install --upgrade pip
   > pip install --upgrade setuptools
   

6. Install pyhamilton.

   pip install pyhamilton
   

7. Run the pyhamilton autoconfig tool from the command line.

   pyhamilton-config
   

   Press accept to proceed with the bundled installers.

8. Run. If you have other Python versions installed, always run pyhamilton with py yourmethod.py (the bundled Python launcher, which interprets shebangs) or python3 yourmethod.py

1. If you encounter an error relating to HxFan (i.e., your robot does not have a fan), open pyhamilton/star-oem/VENUS_Method/STAR_OEM_Test.med, navigate to the "HxFan" grouping, and delete all commands under this grouping.

2. If you would like to test your PyHamilton installation on a computer not connected to a Hamilton robot, use HamiltonInterface(simulate=True) to open your interface inside your robot script.

3. If your initialization hangs (such as on initial_error_example.py), try these steps:
   a. Make sure you don't have any other program running which is communicating with the robot e.g. Venus run control
   b. Make sure the .dlls referenced in __init__.py are unblocked. See this StackOverflow thread for more details.

Please see the list of Ongoing Projects for information on other issues with PyHamilton

PyHamilton is an open-source project, and we have a ton of work to do! If you'd like to contribute to the PyHamilton project, please consider these following areas of ongoing work and don't hesitate to reach out if you want to discuss collaborating with the team.

• Project Manager and Repository: Sharing Hamilton scripts is a hassle, which hinders community development and reproducibility. We are working on a centralized repository where users can upload their PyHamilton projects to share with the rest of the community, along with a simple command-line API for managing projects.

• PyHamilton for Nimbus: Right now PyHamilton only works on the STAR line of liquid-handling robots, but we have recently received the appropriate libraries for expanding the framework to Hamilton Nimbus, a much more affordable and low-footprint robot. This project is in its very early stages so collaborators will have the opportunity to influence crucial design decisions.

• PyHamilton for Linux: One of the biggest limitations for PyHamilton, Hamilton robots, and much of lab automation in general is their exclusive dependence on Windows as an operating system. We are working to recreate the Venus application (which runs on Windows and which PyHamilton depends on in turn) as a Python library, so that PyHamilton will effectively become OS-agnostic. This is a truly massive undertaking but we have made considerable progress due to incredibly talented team member Rick Wierenga.

• A high-throughput platform for feedback-controlled directed evolution, preprint

• Flexible open-source automation for robotic bioengineering, preprint

Developed for the Sculpting Evolution Group at the MIT Media Lab