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An overview of the CellML API and its implementation.

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A new application programming interface (API) and its open-source implementation facilitate the processing and sharing of CellML mathematical models. This tool simplifies complex CellML features, accelerating scientific development and model integration.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Scientific Modeling

Background:

  • CellML is an XML-based language for representing mathematical models in a machine-independent format.
  • Exchanging and archiving computer-readable models is crucial for bioinformatics, improving accuracy and enabling model integration.
  • Developing tools to process complex CellML features like imports can be challenging, necessitating a robust API.

Purpose of the Study:

  • To develop an application programming interface (API) for processing CellML models.
  • To provide a high-performance, Free/Open Source implementation of the CellML API.
  • To facilitate the creation of tools for CellML model exchange and analysis.

Main Methods:

  • Developed a core API for retrieving and modifying information within CellML models.
  • Created optional extension APIs for handling variable connections, physical units, model validation, and code translation.
  • Implemented a Free/Open Source version of the API, optimized for performance.

Main Results:

  • A functional API and its extensions have been developed for CellML model manipulation.
  • A performant, open-source implementation of the API is available.
  • Tools built with the API are mature and ready for broad adoption.

Conclusions:

  • The developed API and its implementation support widespread use and accelerate the creation of new CellML processing tools.
  • This advancement has the potential to significantly increase the sharing of mathematical model descriptions in science.
  • The API addresses the need for accessible tools to manage complex CellML files.