Joseph L. Hellerstein

Antimony 3 updates the human-readable modeling language to support SBML Level 3 features, enabling unified model definitions with kinetic reactions, uncertainty, annotations, and visualizations.

The paper updates and corrects SED-ML files for 1055 models in BioModels to improve reproducibility and verification across simulation engines.

SBMLNetwork provides a framework for standards-based visualization of biochemical models by automating the generation of SBML-compliant visualization data.

AMAS predicts annotations for SBML model elements using reference databases and similarity scores, achieving 80-95% accuracy for species and reactions.

This paper analyzes the frequency response and sensitivity of biochemical cascades with varying phosphorylation layers and states.

SBMate evaluates annotation quality in systems biology models using coverage, consistency, and specificity metrics on 1,000 BioModels repository models.

The paper introduces two new methods for detecting and isolating mass balance errors in reaction-based models, improving error isolation compared to existing approaches.

This paper infers reaction networks from perturbation data using an evolutionary strategy that evolves network topologies and parameters to match experimental data.

Tellurium Notebook enables reproducible and reusable dynamical models in systems biology by integrating community standards and literate coding practices.