libRoadRunner: a high performance SBML simulation and analysis library. - Endre T. Somogyi; Jean-Marie Bouteiller; James A. Glazier; Matthias König 003; J. Kyle Medley; Maciej H. Swat; Herbert M. Sauro (Bioinform., 2015)

phraSED-ML: A paraphrased, human-readable adaptation of SED-ML. - Kiri Choi; Lucian P. Smith; J. Kyle Medley; Herbert M. Sauro (J. Bioinform. Comput. Biol., 2016)

Guidelines for Reproducibly Building and Simulating Systems Biology Models. - J. Kyle Medley; Arthur P. Goldberg; Jonathan R. Karr (IEEE Trans. Biomed. Eng., 2016)

Toward Community Standards and Software for Whole-Cell Modeling. - Dagmar Waltemath; Jonathan R. Karr; Frank T. Bergmann; Vijayalakshmi Chelliah; Michael Hucka; Marcus Krantz; Wolfram Liebermeister; Pedro Mendes 001; Chris J. Myers; Pinar Pir; Begum Alaybeyoglu; Naveen K. Aranganathan; et al. (IEEE Trans. Biomed. Eng., 2016)

A portable structural analysis library for reaction networks. - Yosef Bedaso; Frank T. Bergmann; Kiri Choi; Kyle Medley; Herbert M. Sauro (Biosyst., 2018)

Tellurium: An extensible python-based modeling environment for systems and synthetic biology. - Kiri Choi; J. Kyle Medley; Matthias König 003; Kaylene Stocking; Lucian P. Smith; Stanley Gu; Herbert M. Sauro (Biosyst., 2018)

Tellurium notebooks - An environment for reproducible dynamical modeling in systems biology. - J. Kyle Medley; Kiri Choi; Matthias König 003; Lucian P. Smith; Stanley Gu; Joseph L. Hellerstein; Stuart C. Sealfon; Herbert M. Sauro (PLoS Comput. Biol., 2018)

libsbmljs - Enabling web-based SBML tools. - J. Kyle Medley; Joseph L. Hellerstein; Herbert M. Sauro (Biosyst., 2020)

A compiler for biological networks on silicon chips. - J. Kyle Medley; Jonathan J. Y. Teo; Sung Sik Woo; Joseph L. Hellerstein; Rahul Sarpeshkar; Herbert M. Sauro (PLoS Comput. Biol., 2020)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (CoRR, 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (Nucleic Acids Res., 2022)