Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages

Area of Science:

• Systems Biology
• Computational Biology
• Bioinformatics

Background:

• Biological models require standardized formats for software compatibility, but these are often difficult for humans to read or write.
• The original Antimony language provided a human-readable alternative for defining models, converting to Systems Biology Markup Language (SBML).
• Evolving SBML standards and modeling practices necessitated an update to Antimony to maintain relevance and compliance.

Purpose of the Study:

• To introduce Antimony 3, a comprehensive update to the Antimony language.
• To enhance support for SBML Level 3 packages, including Flux Balance Constraints (FBC), Distributions, Layout, and Render.
• To enable unified model specification combining kinetic reactions, constraint-based analysis, uncertainty representation, annotations, and visualizations in a plain-text format.

Main Methods:

• Formalizing cumulative improvements from previous Antimony versions.
• Extending Antimony's grammar and parser to support new SBML Level 3 features.
• Developing Antimony 3 as a C/C++ library with a stable C API.
• Providing official bindings for Python, Julia, and JavaScript/WebAssembly.
• Releasing a cross-platform desktop GUI for Antimony 3.

Main Results:

• Antimony 3 offers formal support for SBML Level 3 Core and FBC, Distributions, Layout, and Render packages.
• Models can now integrate kinetic reactions with flux balance analysis, incorporate probability distributions for uncertainty, and include semantic annotations.
• Antimony 3 facilitates the creation of publication-ready model visualizations within the same plain-text format.
• The software is available as a lightweight C/C++ library with bindings for multiple programming languages and a desktop GUI.

Conclusions:

• Antimony 3 significantly advances the capability and accessibility of defining complex biological models.
• It provides a unified, human-readable format for diverse modeling approaches, from kinetic to constraint-based.
• The broad availability across computational environments ensures Antimony 3 supports a wide range of research workflows in systems biology.