An Update to the SBML Human-Readable Antimony Language

TL;DR

This paper presents an update to the Antimony language, enhancing its features for systems biology modeling, including new annotations, analysis support, and multi-language distributions to improve model sharing and reproducibility.

Contribution

The paper introduces significant new features and multi-language support for Antimony, making it more versatile and accessible for systems biology modeling since its original 2009 release.

Findings

Added support for flux balance analysis

Introduced new annotation and probability distribution features

Distributed as a C/C++ library with multiple language bindings

Abstract

Antimony is a high-level, human-readable text-based language designed for defining and sharing models in the systems biology community. It enables scientists to describe biochemical networks and systems using a simple and intuitive syntax. It allows users to easily create, modify, and distribute reproducible computational models. By allowing the concise representation of complex biological processes, Antimony enhances collaborative efforts, improves reproducibility, and accelerates the iterative development of models in systems biology. This paper provides an update to the Antimony language since it was introduced in 2009. In particular, we highlight new annotation features, support for flux balance analysis, a new rateOf method, support for probability distributions and uncertainty, named stochiometries, and algebraic rules. Antimony is also now distributed as a C/C++ library, together with python and Julia bindings, as well as a JavaScript version for use within a web browser. Availability: https://github.com/sys-bio/antimony.