xml2jupyter: Mapping parameters between XML and Jupyter widgets

Area of Science:

• Computational Biology
• Scientific Software Development
• Bioinformatics

Background:

• Scientific simulations often rely on text-based configuration files, posing usability challenges for non-technical users.
• Manual editing of these files for parameter exploration is time-consuming and error-prone.
• Jupyter Notebooks offer an interactive environment, but integrating them with existing simulation workflows requires specialized tools.

Purpose of the Study:

• To develop a Python package, xml2jupyter, that bridges the gap between XML configuration files and interactive Jupyter widgets.
• To enable the automatic generation of graphical user interfaces (GUIs) for scientific simulations directly from their configuration files.
• To enhance the accessibility and usability of complex scientific simulation packages for a broader range of users.

Main Methods:

• The xml2jupyter package maps Extensible Markup Language (XML) configuration files to Jupyter widgets.
• Widgets are automatically generated from XML schemas, allowing users to modify simulation parameters interactively.
• Generated widgets can be integrated into larger GUIs and optionally hosted on cloud platforms.

Main Results:

• xml2jupyter successfully generates interactive GUIs from XML configuration files for scientific simulations.
• The package has been successfully tested with PhysiCell, an agent-based biological simulator.
• The tool facilitates classroom use and research projects, improving user experience and accessibility.

Conclusions:

• xml2jupyter significantly lowers the barrier to entry for using complex scientific simulation software.
• The package enhances the ability of researchers and students to explore simulation parameters and conduct research.
• xml2jupyter promotes wider adoption and application of simulation tools like PhysiCell.