SimBOL: SBOL Designs, Ready for Simulation

Or, open the CellModeller converter: https://colab.research.google.com/drive/1v3NV6Cz5RNTp0xLkVwg4ztZ84HLNHoOI#scrollTo=MonufBDOShn7

This tool automates the conversion of genetic circuit designs from SBOL3 format (v3.1.0) into files ready for simulation.

How does it do it?

SimBOL uses two-step process:

1. First, it translates your SBOL3 design into a optimized, easy-to-understand JSON format. This JSON as a clear, concise summary of your circuit – much simpler to work with than raw SBOL3.
2. This special JSON then acts as a universal key, ready to be used by different simulator-specific "plugins".

What's SimBOL All About?

This tool connects the specification of a design—that is, its components, how they interconnect, and the function they must perform—with various simulators to predict its actual behavior.

The process works as follows: an initial design file is first transformed into an optimized and summarized JSON. This JSON then serves as a standardized input for different plugins, each developed for a specific simulator. If necessary, this configuration can be supplemented by a user interface or an additional parameter file, allowing for the adjustment of specific details that each simulator plugin needs to operate correctly.

How It's Organized

The project is set up to be modular, which is just a fancy way of saying it's in logical pieces:

• sbol3_to_json_converter/: This is where the first step happens – reading SBOL3 and creating that optimized JSON.
  • process_sbol.py: The brains of the SBOL processing and JSON creation.
  • upload_sbol_file.py: A little helper for uploading files in Colab.
  • rdf_parser.py, clean_json.py: Other helper bits. COMPLETAR AQUÍ
• json_to_gro_generator/: This section is all about the GRO-specific plugin.
  • gro_file_compiler.py: Takes the JSON and your settings to build the .gro file.
  • params.py: Gets all the GRO-specific details ready.
  • ui_parameters.py: Creates the interactive settings panel for GRO.
• example_data/: Sample SBOL3 files to try, plus examples of the intermediate JSON and the final .gro files.
• README.md
• USER_MANUAL_GRO_PLUGIN.md: For more detailed instructions of gro plugin.

Get Started with SimBOL's GRO Plugin

The simplest way to try out SimBOL (using the GRO plugin) is directly with our public Google Colab notebook.

1. Open in Colab:     * Click the badge below to open the notebook directly in Google Colab:

2. Run the Notebook:

   • Simply follow the instructions within the notebook and run the cells in order. The notebook will handle the entire process:
     • Cloning the SimBOL repository and installing all necessary dependencies.
     • Allowing you to upload your design file in SBOL3 format.
     • Automatically converting your SBOL3 design into the optimized intermediate JSON format (which will also be downloaded for you to review).
     • Displaying the user-friendly interface for you to configure GRO-specific parameters.
     • Generating your simulation-ready .gro file and and downloading it automatically.

License

This project is shared under the MIT License.