Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology

Area of Science:

• Systems biology
• Computational biology
• Biomedical modeling

Background:

• Reproducing published dynamical models is challenging, hindering validation and reuse.
• Lack of standardization complicates model sharing and integration in biomedical research.

Purpose of the Study:

• To develop a software system, Tellurium Notebook, to improve reproducibility and reuse of dynamical models.
• To facilitate model authoring, simulation, and teaching within a unified environment.

Main Methods:

• Developed Tellurium Notebook, a Python-based Jupyter-like environment.
• Integrated model authoring, simulation, and narrative in a notebook format.
• Supported the COMBINE archive format for model exchange and interoperability.

Main Results:

• Tellurium Notebook allows intermixing of models, Python code, and narrative.
• Automated conversion between COMBINE standards and human-readable formats.
• Enabled in-line simulation, editing, and re-export of COMBINE-compliant models.

Conclusions:

• Tellurium Notebook enhances dynamical model development, reproducibility, and reuse.
• The system lowers the technical barrier for using and modifying standardized models.
• Facilitates easier exploration of model dynamics, variants, and test cases.