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.

Please post on labautomation.io if you have any questions, comments, issues, or feedback! You can also email stefanmgolas@gmail.com for troubleshooting help.

Disclaimer: PyHamilton is not officially endorsed or supported by the Hamilton Company. Please direct any questions to the above email address, and not to Hamilton Company.

if __name__ == "__main__":

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

Here is a protocol repository with guides about how to do things like magnetic bead washes and thermal cycling. These are all NGS protocols, but you can use the same steps in many other experiments.

NGS Protocol Library

Available online.

https://www.youtube.com/watch?v=G92neaVfvyw

1. Install and test the standard Hamilton software suite for your system. We no longer host the link here, please contact Hamilton for a copy of the Venus software if you don't have one already

2. Install Python <=3.13. Make sure to check the box that asks if you want to add Python to your path variable.

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. Install Microsoft Access database engine. This must have the same bit number (32-bit or 64-bit) as your Python version, and the rest of your Microsoft Office applications.

6. Update your pip and setuptools.

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

7. Install pyhamilton.

   git clone https://github.com/dgretton/pyhamilton
   cd pyhamilton
   pip install -e .
   

   Now changes you make to the cloned repo will be reflected in your package install. You can test new code this way and then push it to a fork.

8. Run the pyhamilton autoconfig tool from the command line. This will automatically execute all the installers in pyhamilton/bin and will copy all the files in pyhamilton\library to C:/Program Files (x86)/HAMILTON/Library. You are welcome to forgo this command and perform the steps manually if you are concerned about file overwriting.

   pyhamilton-configure
   

   Press accept to proceed with the bundled installers.

9. Test your PyHamilton installation
   The easiest way to test your PyHamilton installation is by running the following in your terminal

   mkdir new-project
   cd new-project
   pyhamilton-new-project
   py robot_method.py
   

10. 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.

4. If you get an error like pyhamilton-configure is not recognized as an internal or external command, operable program or batch file, make sure the directory containing your Python interpreter is in your path environment variable.

• 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