JSim, an open-source modeling system for data analysis. - Erik Butterworth; Bartholomew Jardine; Gary M. Raymond; Maxwell Lewis Neal; James B. Bassingthwaighte (F1000Research, 2013)

Semi-automated Modular Program Constructor for physiological modeling: Building cell and organ models. - Bartholomew Jardine; Gary M. Raymond; James B. Bassingthwaighte (F1000Research, 2015)

MakeSBML: a tool for converting between Antimony and SBML. - Bartholomew E. Jardine; Lucian P. Smith; Herbert M. Sauro (J. Integr. Bioinform., 2024)